In the past few days, President Trump has bulldozed the already faltering tradition of Justice Department independence from the White House.

First, he ousted a U.S. attorney who failed to file charges against his political enemies. Then he followed up that extraordinary move with two others, demanding — in public — that his attorney general go after his adversaries and replacing the career prosecutor who did not meet his demands with an inexperienced loyalist.

But while the president has openly pressured the Justice Department into charging those he sees as his foes, the criminal justice system he is seeking to control has a few guardrails that lie beyond his reach and could ultimately stop or delay him.

Mr. Trump might want to snap his fingers and see opponents like Letitia James, the New York State attorney general, and James B. Comey, the former F.B.I. director, quickly charged, convicted and put behind bars, but that is not the way the system works.

“Federal criminal prosecutions require ‘robust procedural safeguards,’” Justice Sonia Sotomayor wrote last summer in her stinging dissent to a Supreme Court ruling granting Mr. Trump broad immunity from criminal charges.

“Bare allegations of malice would not make it out of the starting gate,” Justice Sotomayor went on. “Although a private civil action may be brought based on little more than ‘intense feelings,’ a federal criminal prosecution is made of firmer stuff.”

Here is a look at some of that stuff — the safeguards in the system that could give pause to Mr. Trump’s moves for revenge.

Prosecutorial Norms

Federal prosecutors are bound by Justice Department policy to pursue impartial prosecutions, founded not on whims or partisan politics, but only on the facts and the law.

Their discretion and probity is meant to be the first line of defense against purely vengeful charges being filed. They are supposed to bring indictments only if they serve the interests of justice and they believe they can obtain a conviction and sustain it on appeal.

Such norms, of course, while rooted in tradition, do not carry the force of law, and can be broken outright or altered over time. Erik S. Siebert was ousted from his post last week atop the U.S. attorney’s office in the Eastern District of Virginia after failing to indict Ms. James and Mr. Comey.

It remains unclear what sort of prosecutor Mr. Siebert’s successor, Lindsey Halligan, who worked as Mr. Trump’s personal lawyer, will be.

Still, U.S. attorneys and their subordinates can stick to principles, even if the only way to do so is to quit their jobs if they are asked to do something improper or illegal. That, in fact, has happened several times during Mr. Trump’s second term in office.

In February, Danielle R. Sassoon resigned as the interim U.S. attorney in Manhattan rather than obey an order from a top Justice Department official to drop the corruption case against New York City’s mayor, Eric Adams.

And in May, Ben Schrader, a top prosecutor in the U.S. attorney’s office in Nashville, left his job, court papers say, rather than bring a “vindictive prosecution” against Kilmar Armando Abrego Garcia, the immigrant who was wrongfully deported to El Salvador in March and returned to U.S. soil to face indictment.

Grand Juries

Prosecutors cannot simply will indictments into being. To charge someone with a felony, they have to persuade a grand jury composed of ordinary citizens that there is at least some evidence a crime was committed.

While the evidentiary threshold is low, grand juries still serve as a check on prosecutorial power. An old saying holds that prosecutors are in such complete control of grand jurors that they could get them to indict a ham sandwich if they wanted. But recent events in Washington and Los Angeles have proved that isn’t always true.

In the past two months, grand jurors in Federal District Court in Washington have repeatedly refused to indict fellow residents who became entangled in either Mr. Trump’s immigration crackdown or in his efforts to flood the city’s streets with federal troops and agents. The rejections occurred in at least eight cases, including three separate times for the same defendant.

Something similar took place in Los Angeles this summer as grand jurors declined to approve indictments against several people arrested during protests against local immigration raids. Many of the defendants had, like those in Washington, been accused of assaulting the authorities.

Taken together, the pushback from grand jurors looked a lot like a bicoastal revolt against prosecutors seeking to file harsh charges against local residents in an atmosphere of anger or distress over Mr. Trump’s political agenda.

It remains unclear whether grand jurors in Virginia might do the same if they have to consider felony charges against Ms. James or Mr. Comey. Grand jurors in Maryland could also face an analogous situation if prosecutors seek to obtain an indictment in another case that Mr. Trump has pushed against Senator Adam B. Schiff, Democrat of California.

Judicial Review

If any of these cases do reach indictment, defense lawyers would move quickly to challenge the charges with motions to dismiss in what would amount to a third line of defense against the prosecution.

At this stage, Mr. Trump’s own words could come back to haunt him.

On social media over the weekend, Mr. Trump preemptively declared that Ms. James, Mr. Comey and Mr. Schiff were “all guilty as hell, but nothing is going to be done.” An unfounded statement like that could easily be featured in a motion accusing the Justice Department of taking part in an improperly vindictive prosecution.

Such motions are notoriously difficult to win, and yet the defense has recently filed them in a handful of high-profile cases in which the president and his top aides have made public statements suggesting a political animus against the defendant.

In Mr. Abrego Garcia’s case, lawyers accused the government of bringing charges against him only after he fought his initial deportation. They also said administration officials had made incessant attacks against their client, calling him a “gangbanger,” “monster,” “illegal predator,” “illegal alien terrorist” and “human trafficker.”

Mr. Siebert’s ouster in Virginia could also wind up being used in an effort to discredit a potential prosecution. Defense lawyers could make hay out of the fact that the man who once ran the prosecutors’ office clearly had qualms about bringing charges.

Costs of an Offensive, Nonetheless

While all of these guardrails offer some measure of protection against wrongful or malicious prosecution, sometimes, as criminal justice experts say, the process is the punishment.

Even if a prosecution is dismissed or does not pan out, facing criminal charges — especially from a powerful federal government — can be extremely stressful, painfully expensive and deeply damaging to personal reputation.

One of Mr. Trump’s close allies, Ed Martin, who runs the so-called weaponization working group, which was created to go after the president’s opponents, admitted earlier this year that he plans to use his authority to expose and discredit those he believes to be guilty, even if he cannot find sufficient evidence to prosecute.

“If they can be charged, we’ll charge them,” Mr. Martin told reporters in May. “But if they can’t be charged, we will name them. And we will name them, and in a culture that respects shame, they should be people that are ashamed.”